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De-lint propka/atom.py

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Other changes are a result of Atom use in other files.
This commit is contained in:
Nathan Baker
2020-05-17 17:08:38 -07:00
parent 303aaae25a
commit 10efc3c7f9
10 changed files with 178 additions and 177 deletions
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14
propka/conformation_container.py
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@@ -158,7 +158,7 @@ class Conformation_container:
titrate_only = self.molecular_container.options.titrate_only
if titrate_only is not None:
at = group.atom
if not (at.chainID, at.resNumb, at.icode) in titrate_only:
if not (at.chain_id, at.res_num, at.icode) in titrate_only:
group.titratable = False
if group.residue_type == 'CYS':
group.exclude_cys_from_results = True
@@ -376,7 +376,7 @@ class Conformation_container:
return [atom for atom in self.atoms if atom.type=='hetatm' and atom.element != 'H']
def get_chain(self,chain):
return [atom for atom in self.atoms if atom.chainID != chain]
return [atom for atom in self.atoms if atom.chain_id != chain]
def add_atom(self, atom):
@@ -388,13 +388,13 @@ class Conformation_container:
atom.molecular_container = self.molecular_container
# store chain id for bookkeeping
if not atom.chainID in self.chains:
self.chains.append(atom.chainID)
if not atom.chain_id in self.chains:
self.chains.append(atom.chain_id)
return
def copy_atom(self, atom):
new_atom = atom.makeCopy()
new_atom = atom.make_copy()
self.atoms.append(new_atom)
new_atom.conformation_container = self
@@ -443,8 +443,8 @@ class Conformation_container:
return
def sort_atoms_key(self, atom):
key = ord(atom.chainID)*1e7
key += atom.resNumb*1000
key = ord(atom.chain_id)*1e7
key += atom.res_num*1000
if len(atom.name) > len(atom.element):
key += ord(atom.name[len(atom.element)])
#info(atom,ord(atom.name[len(atom.element)]), '|%s||%s|'%(atom.name,atom.element))